Modern air vehicles face increasing internal heat loads that must be appropriately understood in design and managed in operation. This paper examines one solution to creating more efficient and effective thermal management systems (TMSs): vapor cycle systems (VCSs). VCSs are increasingly being investigated by aerospace government and industry as a means to provide much greater efficiency in moving thermal energy from one physical location to another. In this work, we develop the AFRL (Air Force Research Laboratory) Transient Thermal Modeling and Optimization (ATTMO) toolbox: a modeling and simulation tool based in Matlab/Simulink that is suitable for understanding, predicting, and designing a VCS. The ATTMO toolbox also provides capability for understanding the VCS as part of a larger air vehicle system. The toolbox is presented in a modular fashion whereby the individual components are presented along with the framework for interconnecting them. The modularity allows for easy user re-configurability as well as the ability to scale from simple to full vehicle systems. A computational environment is discussed that allows for simulations running many times faster than real-time. Simulation results are presented for a laboratory scale test stand system consisting of both single and multiple evaporators. The simulations are verified against experimental results demonstrating the potential of the tool.